Engineering of metabolic control

ABSTRACT

The invention features a method of producing heterologous molecules in cells under the regulatory control of a metabolite and metabolic flux. The method can enhance the synthesis of heterologous polypeptides and metabolites.

This application claims the benefit of U.S. provisional application60/145,801, filed Jul., 27, 1999.

GOVERNMENT RIGHTS

This invention was made with Government support under GrantDE-FG03-98ER20298 with the U.S. Department of Energy and GrantBES-9814097 with the National Science Foundation. The Government hascertain rights in the invention.

BACKGROUND OF THE INVENTION

The use of recombinant DNA technology has allowed the engineering ofhost cells to produce desired compounds, such as polypeptides andsecondary metabolites. The large scale production of polypeptides inengineered cells allows for the production of proteins withpharmaceutical uses and enzymes with industrial uses. Secondarymetabolites are products derived from nature that have long been knownfor their biological and medicinal importance. Because of the structuralcomplexity inherent in such molecules, traditional chemical synthesisoften requires extensive effort and the use of expensive precursors andcofactors to prepare the compound. In recent years, the expression ofheterologous proteins in cells has facilitated the engineering ofheterologous biosynthetic pathways in microorganisms to producemetabolites from inexpensive starting materials. In this manner, avariety of compounds have been produced, including polyketides, β-lactamantibiotics, monoterpenes, steroids, and aromatics.

SUMMARY OF THE INVENTION

The invention is based, in part, on the discovery that production ofheterologous polypeptides and metabolites can be enhanced by theregulated expression of the polypeptide (e.g., a biosynthetic enzyme)using a promoter which is regulated by the concentrations of a secondmetabolite, e.g. acetyl phosphate. The term “heterologous” refers to apolypeptide or metabolite which is introduced by artifice. Aheterologous polypeptide or metabolite can be identical to endogenousentity that is naturally present. The term “metabolite” refers to aorganic compound which is the product of one or more biochemicalreactions. A metabolite may itself be a precursor for other reactions. Asecondary metabolite is a metabolite derived from another.

Accordingly, in one aspect, the invention features a bacterial host cellcontaining a nucleic acid sequence comprising a promoter and a nucleicacid sequence encoding a heterologous polypeptide. Examples of bacterialhost cells include Escherichia coli, Bacillus subtilis, Salmonellatyphimurium, Agrobacterium tumefaciens, Thermus thermophilus, andRhizobium leguminosarum cells. The nucleic acid sequence is operablylinked to the promoter which is controlled by a response regulatorprotein. In other words, the nucleic acid sequence is linked to thepromoter sequence in a manner which allows for expression of thenucleotide sequence in vitro and in vivo. “Promoter” refers to any DNAfragment which directs transcription of genetic material. The promoteris controlled by a response regulator protein, for example, ntrC, phoB,phoP, ompR, cheY, creB, or torR, of E. coli or its homologs from otherbacterial species. Further, the response regulator protein can beanother member of the cluster orthologous group (COG) COG0745 as definedby www.ncbi.nlm.nih.gov/COG/(Tatusov et al. Nucleic Acids Res. (2000);28:33–36). In one implementation, the promoter is bound by E. coli ntrC.The term “ntrC” refers to both the E. coli ntrC protein (SWISSPROT:P06713) www.expasy.ch/ and its homologs in other bacteria asappropriate. As used herein, “bound” refers to a physical associationwith a equilibrium binding constant (K_(D)) of less than 100 nM,preferably less than 1 nM. An example of the promoter is the E. coliglnAp2 promoter, e.g. a region between positions about 93 and about 323in the published DNA sequence, GenBank accession no. M10421(Reitzer &Magasanik (1985) Proc Nat Acad Sci USA 82:1979–1983). This regionincludes untranslated sequences from the glnA gene. Further, atranslational fusion can be constructed between coding sequences forglnA and coding sequences for the heterologous polypeptide.

The host cell is genetically modified such that the promoter isregulated by acetyl phosphate in the absence of nitrogen starvation. Forexample, the host cell can genetically modified by deletion or mutationof a gene encoding a histidine protein kinase, e.g., a member of COG0642as defined by (http://www.ncbi.nlm.nih.gov/COG/; Tatusov et al. supra.),e.g., glnL, phoR, phoQ, creC, or envZ. In another example, the histidineprotein kinase has specificity for the response regulator protein whichcontrols the promoter. The histidine protein kinase can be encoded byglnL, e.g., E. coli glnL (SWISSPROT P06712; www.expasy.ch/).

Whereas the host cell is genetically modified such that the promoter isregulated by acetyl phosphate in the absence of nitrogen starvation, forheterologous polypeptide or metabolite expression, the host cell can bepropagated in any desired condition, e.g., in nitrogen starvationconditions, nitrogen poor conditions, or nitrogen rich conditions.

The heterologous polypeptide encoded by the nucleic acid sequence can bea biosynthetic enzyme required for production of a metabolite. It can bea mammalian protein, e.g., a secreted growth factor, a monoclonalantibody, or an extracellular matrix component. In yet another example,the heterologous polypeptide can be a desired antigen for use in avaccine, e.g., a surface protein from a viral, bacterial, fungal, orprotist pathogen.

Another aspect of the invention features a kit containing a nucleic acidsequence which includes a promoter controlled by a response regulatorprotein. The kit further optionally contains a bacterial host cell whichis genetically modified such that the promoter is regulated by acetylphosphate in the absence of nitrogen starvation. The kit can alsoprovide instructions for their use. The nucleic acid sequence cancontain a restriction enzyme polylinker located 3′ of the promoter suchthat a sequence inserted into the polylinker is operably linked to thepromoter which is controlled by a response regulator protein. In oneimplementation of the kit, the promoter is the E. coli glnAp₂, promoterand the bacterial host cell is an E. coli cell containing a mutation ordeletion of the glnL gene.

Another aspect of the invention features a host cell containing a firstexpression cassette. The first expression cassette includes a promoter,such as any of those described above, and a nucleic acid sequenceencoding an enzyme required for biosynthesis of a heterologousmetabolite. As used herein, “enzyme” refers to a polypeptide havingability to catalyze a chemical reaction or multiple reactions. Thenucleic acid sequence is operably linked to the promoter which isregulated by acetyl phosphate in the absence of nitrogen starvation. Thehost cell also contains additional nucleic acid sequences for expressingother enzymes required for biosynthesis of the metabolite. Suchadditional sequences may be endogenous sequences expressing endogenousenzymes, or introduced sequences expressing heterologous enzymes.

In one example, the heterologous metabolite is an isoprenoid, apolyhydroxyalkanoate, a polyketide, a β-lactam antibiotic, an aromatic,or a precursor, e.g., an upstream metabolite, or a derivative, e.g., adownstream metabolite, thereof. For instance, the isoprenoid can be acarotenoid, a sterol, a taxol, a diterpene, a gibberellin, and aquinone. Specific examples of isoprenoids include isopentyl diphosphate,dimethylallyl diphosphate, geranyl diphosphate, farnesyl diphosphate,geranylgeranyl diphosphate, and phytoene. Specific examples ofcarotenoids include β-carotene, ξ-carotene, astaxanthin, zeaxanthin,zeaxanthin-β-glucoside, phytofluene, neurosporene, lutein, and torulene.When the desired heterologous metabolite is an isoprenoid, theheterologous enzyme can be isopentenyl diphosphate isomerase,geranylgeranyl diphosphate synthase, or 1-deoxyxylulose 5-phosphatesynthase. When the desired heterologous metabolite is anpolyhydroxyalkanoate, the heterologous enzyme can be 3-ketoacylreductase, or poly-3-hydroxyalkanoate polymerase.

The host cell can be a bacterial cell, e.g., an E. coli cell. The hostcell is optionally genetically modified by deletion or mutation of agene, e.g., a gene encoding a histidine protein kinase, as describedabove. In one specific example, the host cell further contains a secondexpression cassette containing a nucleic acid sequence encodingphosphoenolpyruvate synthase operably linked to a promoter regulated byacetyl phosphate concentration, e.g., glnAp₂.

Another aspect of invention features a method of producing heterologousisoprenoids in a host cell. The method includes overexpressingphosphoenolpyruvate synthase and expressing biosynthetic enzymesrequired for synthesis of the heterologous isoprenoid. In oneimplementation, a gene in the host cell encoding a pyruvate kinase or aphosphoenolpyruvate carboxylase is genetically deleted or enfeebled. Inanother implementation, a gene encoding phosphoenolpyruvatecarboxykinase is overexpressed in the host cell. Still another aspect ofthe invention features a method of producing a lycopene in a host cell.The method includes expressing the following heterologous enzymes:1-deoxy-D-xylulose 5-phosphate synthase, a geranylgeranyl diphosphatesynthase, a phytoene synthase, and a phytoene saturase. In oneimplementation of this method, an isopentenyl diphosphate isomerase isoverexpressed, e.g., using the glnAp2 promoter. In anotherimplementation, a phosphoenolpyruvate synthase is overexpressed, e.g.,using the glnAp2 promoter.

Another aspect of the invention features a nucleic acid sequencecontaining a promoter and a sequence encoding a biosynthetic enzymerequired for the production of a first metabolite. The promoter isoperably linked to the sequence, and is regulated by a second metabolitewhose concentration is indicative of availability of a precursor for thebiosynthesis of the first metabolite. In one example, the secondmetabolite is a waste product produced from a precursor for thebiosynthesis of the first metabolite.

In one implementation, the first metabolite is a polyhydroxyalkanoate,e.g., polyhydroxybutyrate and the nucleic acid sequence encodes abiosynthetic enzyme, e.g., a 3-ketoacyl coenzyme A (coA) reductases, ora poly-3-hydroxyoctanoyl-CoA polymerase. In another case, the firstmetabolite is a polyketide, a β-lactam antibiotic, or an aromatic. In ayet another case, the first metabolite is an isoprenoid, e.g., anisoprenoid mentioned herein. The nucleic acid sequence can encode abiosynthetic enzyme required for isoprenoid production, e.g.,isopentenyl diphosphate isomerase, geranylgeranyl diphosphate synthase,1-deoxyxylulose 5-phosphate synthase, phosphoenolpyruvate synthase,farnesyl diphosphate synthase, geranylgeranyl diphosphate synthase,phytoene synthase, phytoene desaturase, or lycopene cyclase. Oneprecursor of isoprenoids can be pyruvate. Pyruvate concentrations arerelated to acetate and acetyl-phosphate concentrations. Accordingly, inthis instance, the second metabolite is acetyl phosphate. The promoterresponding to acetyl phosphate can be controlled by a response regulatorprotein, e.g., a response regulator protein mentioned above. Such apromoter may only respond to acetyl phosphate in a specific host cell.In a particular example, the promoter responding to acetyl phosphateconcentration is bound by E. coli ntrC, e.g., E. coli glnAp₂ promoter.

The promoter can be regulated by cAMP. The promoter can be a bacterialpromoter which binds CAP (catabolite activator protein). In mammals, thepromoter can be a promoter containing a cAMP response element (CRE),which binds to the proteins CREB, CREM, or ATF-1. In yeast cells, thepromoter can be a promoter regulated by cAMP, or a promoter bound byproteins Gis1, Msn2, or Msn4. Another possible regulatory signal for thepromoter can be fructose 1-phosphate, or fructose 6-phosphate. The E.coli FruR protein regulates such promoters.

The nucleic acid sequence can be contained on a plasmid. It can alsocontain a bacterial origin of replication and a selectable marker. Thesequence can further contain a yeast or other eukaryotic origin ofreplication and appropriate selectable markers, and can be integratedinto the genome.

The optimization of biosynthesis of heterologous compounds in host cellsis reliant on sensing parameters of cell physiology and on utilizingthese parameters to regulate the biosynthesis. One standard techniquesin the art is to grow cells and for the user to exogenously add anagent, e.g., an inducer, to turn on genes required for biosynthesis ofthe desired product. It has been widely observed that high-levelinduction of a recombinant protein or pathway leads to growthretardation and reduced metabolic activity. (Kurland and Dong (1996) MolMicrobiol 21:1–4). The practice of exogenously supplying an inducer isempirical and does not monitor the availability of resources in the cellfor biosynthesis. In contrast, natural pathways rely on feedbackmechanisms to control such processes. The combination of certainpromoters with specific genetically defined host cells and heterologouspolypeptides in this invention unexpectedly results in a highly refinedand versatile control circuit that regulates flux to heterologouspolypeptide or metabolite synthesis in response to the metabolic stateof the cell. Indeed, the dynamically controlled recombinant pathwayprovides for enhanced production, minimized growth retardation, andreduced toxic by-product formation. The regulation of gene expression inresponse to physiological state will also benefit other applications,such as gene therapy.

The details of one or more embodiments of the invention are set forth inthe description below. Other features, objects, and advantages of theinvention will be apparent from the description and from the claims.

DETAILED DESCRIPTION

The invention provides methods of engineering metabolic control, e.g.,methods of utilizing promoters in specific host cells in order tooptimize protein expression for either protein production or metabolitesynthesis.

A central component of the invention is an expression cassettecomprising a promoter and nucleic acid sequence encoding a heterologouspolypeptide whose expression is desired. The expression cassette isconstructed using standard methods in the art such that the codingnucleic acid sequence is operably linked, e.g., regulated by, thepromoter. The promoter is chosen such that the promoter is regulated bya parameter of cell physiology or cell metabolic state. A variety ofpromoters can be used. In some applications the expression cassette iscontained within a plasmid, such as bacterial plasmid with a bacterialorigin of replication and a selectable marker. The expression cassettecan be integrated into the genome of cells using standard techniques inthe art.

If the expression cassette is to be used for engineering regulatedproduction of a heterologous polypeptide during late logarithmic growthor during stationary phase, then the promoter can be chosen accordingly.For example, a promoter can be chosen that responds to small moleculesignal, e.g., a second messenger, whose levels accumulate during latelogarithmic growth or during stationary phase. The second messenger canbe a molecule that accumulates as a precursor, an intermediate, or awaste product of a biochemical pathway. In bacteria, the small moleculesignal can be a glycolysis intermediate, e.g., fructose 1-phosphate orfructose 6-phosphate or a glycolysis waste product, e.g., acetate oracetyl phosphate. In eukaryotic cells, cAMP concentrations are a wellknown signal of nutrient state.

The promoter in the expression cassette can be chosen based on theresults of a large scale expression analysis experiment, e.g., a genechip experiment. Genes which are induced by acetyl phosphate can beidentified by hybridizing to a microarray labeled cDNA prepared fromcells in grown in acetate and comparing the signal to a referencesignal, e.g., to the signal of obtained with cDNA prepared from cells inearly logarithmic growth. This experiment can be performed on bothprokaryotic and eukaryotic cells, e.g., bacterial, yeast, plant andmammalian cells. For an example of such an experiment in a prokaryote,see Talaat et al. (2000) Nat Biotechnol 18:679–82 and Oh & Liao (2000)Biotechnol Prog. 16:278–86. Once a gene is identified which is expressedunder the desired condition, its promoter can utilized in the expressioncassette. Alternatively, the experiment can be performed by theexogenous addition of a desired molecule (e.g., a precursor in ametabolic pathway) or by manipulation of experimental conditions (e.g.,growth to late logarithmic phase or growth while a biosynthetic enzymeis overproduced). Promoters can be identified based on the genesinduced.

In one instance, an expression cassette is used for engineeringregulated production of a metabolite in a bacterial cell. The promotercan be selected which is regulated by a second metabolite whoseconcentration is indicative of the availability of a precursor for thebiosynthesis of the first metabolite. For example, if the firstmetabolite is an isoprenoid which is synthesized from the precursors,pyruvate and glyceraldhyde 3-phosphate, then the second metabolite canbe acetyl phosphate. In a rich environment, cells produce an excessamount of acetyl-CoA, a product of pyruvate. The excess acetyl-CoA isused to produce ATP and acetate, which is secreted as a waste product.Acetate concentration increases with cell density. Acetate, acetyl-CoA,and acetyl-phosphate concentrations are interrelated by to the followingbiochemical reactions:acetyl-CoA+P_(i)

acetyl phosphate+CoA  (1)acetyl phosphate+ADP

acetate+ATP  (2)

Thus, high acetyl phosphate concentration is indicative of excessacetyl-CoA and excess pyruvate. A host cell which is geneticallymodified by deletion or mutation of glnL, for example, causes ntrCfunction to become acetyl phosphate dependent (Feng et al. (1992) JBacteriol 174:6061–6070). In this fashion, a promoter regulated by ntrC,e.g., the glnAp2 promoter, can be used to control gene expression inresponse to acetyl phosphate. The glnAp2 promoter can be obtained usingstandard techniques in the art. For example, primers can be designed andsynthesized that anneal to the glnAp2 promoter. The polymerase chainreaction (PCR) can be used to amplify a nucleic acid fragment containingthe glnAp2 promoter. This fragment can now be used for furtherconstructions. Likewise, an E. coli strain containing deletion ofhistidine protein kinase gene, e.g., glnL can be easily prepared. SeeLink et al. (1997) J. Bacteriol. 179(20):6228–6237 for a detaileddescription of one possible method. The sequences encoding a desiredheterologous polypeptide can be cloned downstream of the glnAp2 promoterso that it is operably linked to the promoter. A host cell with aninactivated glnL gene can then be transformed with the sequences. Thetransformed strain can be grown, and polypeptide production monitoredduring the course of growth. Robust protein expression can be observedat high cell densities, as in Farmer and Liao (2000) Nat. Biotechnol18:533–537, the contents of which are hereby incorporated by reference.

A mammalian cell can be used as a host cell for polypeptide ormetabolite production. A promoter can be selected, e.g., a promoter thatresponds to cAMP. Such a promoter can contain a cAMP response element(CRE), which binds to the proteins CREB, CREM, or ATF-1. Using standardtechniques in the art, a desired coding sequence can be placed undercontrol of the promoter and transformed into the mammalian cell. In someinstances, the construction can be inserted into a virus, e.g., aninactivated virus. Such implementations allow for the regulatedproduction of a protein or a metabolite produced by a heterologousbiosynthetic enzyme in a gene therapy scenario. Plant cells can also beused as host cells. Again, an appropriate promoter can be chosen, e.g.,a promoter than responds to a plant hormone, metabolite, or a precursorfor the production of a desired metabolite. A promoter can be identifiedby a microarray experiment. After fusion of a desired promoter to adesired coding sequence in an appropriate vector, the construction canbe electroporated into Agrobacterium tumefaciens and then used totransform plant cells using standard methods in the art. In stillanother example, yeast cells can be manipulated to express heterologouspolypeptides or metabolites under metabolic control. For example, aSaccharomyces cerevisiae promoter can be a promoter regulated by cAMP,e.g., a promoter bound by proteins Gis1, Msn2, or Msn4. The regulationof all yeast genes in response to a variety of metabolic conditions isincreasingly well studied. For example, DeRisi et al. (1997) Science278:680–686 describe experiments following the transcriptional profileof nearly the entire Saccharomyces cerevisiae gene set under variousmetabolic conditions. Promoters regulated by a desired metabolite can beselected based on such data. The generation of yeast plasmids and thetransformation of yeast are well known in the art.

A variety of metabolic pathways can be reconstructed using theexpression techniques described above. For example, a pathway to producelycopene can be introduced in E. coli by constructing expression vectorsfor the following genes: dxs (coding for 1-deoxy-D-xylulose 5-phosphatesynthase) from E. coli, gps (coding for geranylgeranyl diphosphate(GGPP) synthase) from Archaeoglobus fulgidus, and crtBI (coding forphytoene synthase and desaturase, respectively) from Erwinia uredovora.These genes can reside on a single or multiple plasmids, or can beintegrated into the E. coli chromosome. In addition, phosphoenolpyruvatesynthase can be overexpressed using any method, e.g., by fusion to theglnAp2 promoter. Isopentyl diphosphate isomerase can be overexpressedusing any method, e.g., by fusion to the glnAp2 promoter.

In another example, a pathway to produce polyhydroxyalkanoates (PHA),e.g., polyhydroxybutyrate can be implemented in E. coli. PHA is a familyof linear polyesters of hydroxy acids with a variety of thermoplasticproperties and commercial uses. Pseudomonas aeruginosa genes encoding3-ketoacyl coenzyme A reductases and poly-3-hydroxyalkanoate polymerasecan be placed under regulation of a desired promoter, e.g., glnAp2,since acetyl-CoA levels can be indicative of precursor availability forPHA synthesis.

Without further elaboration, it is believed that the above descriptionhas adequately enabled the present invention. The following examplesare, therefore to be construed as merely illustrative, and notlimitative of the remainder of the disclosure in any way whatsoever. Allpublications cited herein are hereby incorporated by reference in theirentirety.

Methods

Growth conditions. All E. coli strains were grown in shake flaskscontaining the designated medium at 37° C. in waterbath shakers (ModelG76; New Brunswick Scientific, Edison, N.J.). The cultures were grown inminimal media consisting of either M9 defined salts 34 containing 0.5%(wt/vol) glucose or YE defined salts containing 1.5% (wt/vol) glucose.YE defined salts consisted of (per liter) 14 g K₂HPO₄, 16 g KH₂PO₄, 5 g(NH₄)₂SO₄, 1 g MgSO₄, and 1 mg thiamine. Cell turbidity was monitoredspectrophotometrically at 550 nm. Metabolite measurements. Acetate,pyruvate, and other organic acids were measured using HPLC (Constametric3500 Solvent Delivery System and Spectromonitor 3100 Variable WavelengthDetector; LDC Analytical, Riviera Beach, Fla.) over an organic acidscolumn (Aminex HPX-87H, Bio-Rad Laboratories, Hercules, Calif.)maintained at 65° C. The mobile phase consisted of 0.01 N H2SO4 and itsflow rate was kept at 0.6 ml min⁻¹. Peaks coming off the column weredetected at 210 nm. Glucose was measured using Sigma kit no. 315–100. Toquantify lycopene, 1 ml of bacterial culture was extracted with acetone,centrifuged, and the supernatant absorbance was measured at 474 nm.Lycopene concentrations were calculated by comparing absorbances to astandard curve.

SDS-PAGE and enzyme assays. The protocol for SDS-PAGE is as described byLaemmli (1970) Nature 227:680–685. Measurement of β-galactosidaseactivity was carried out essentially as described by Miller (1992) AShort Course in Bacterial Genetics, Cold Spring Harbor Laboratory Press,Cold Spring Harbor N.Y.Results

Usage of the glnAP2 promoter in E. coli in a heterologous fusion tolacZ.

Increasing levels of acetyl phosphate can be an indicator of excessglucose flux. The current invention features host cells, nucleic acidssequences, and methods of utilizing acetyl phosphate as a signal toregulate the expression of rate-controlling enzymes in a desiredmetabolic pathway, both to utilize fully the excess carbon flux and toredirect the flux away from the toxic product, acetate.

In order to examine the potential of glnAp2 as a dynamic controller ofproduct expression, a nucleic acid sequence was constructed containing aheterologous lacZ gene operably linked to the glnAp2 promoter. TheglnAp2 promoter region containing the promoter and two ntrC-bindingsites can be easily obtained by standard methods known in the art. TheglnAp2 promoter was PCR-amplified from E. coli genomic DNA using theforward primer 5′-CAGCTGCAAAGGTCATTGCACCAAC (containing an engineeredPvuII site) and the reverse primer 5′-GGTACCAGTACGT-GTTCAGCGGACATAC(containing an engineered KpnI site). These two primers amplified aregion between positions 93 and 343 in the published DNA sequence 16(GenBank accession No. M10421).

The glnAp2 PCR fragment was also cloned into the EcoRI site of pRS551,thus generating p2GFPuv, which contains glnAp2 in front of apromoterless lacZ gene. The glnAp2-lacZ region was transferred to λRS45via homologous recombination (Simons et al.(1987) Gene 53:85–96),generating phage λp2GFPuv. JCL1595 and JCL1596 were constructed byintegrating a glnAp2-lacZ fusion via infection (Silhavy et al. (1984)Experiments with Gene Fusions, Cold Spring Harbor Laboratory Press, ColdSpring Harbor N.Y.) with λp2GFPuv phage into the chromosomes of BW13711(lacX74) and BW18302 (lacX glnL2001, Feng et al. supra), respectively.This strain contains the glnL2001 allele, which consists of an internaldeletion between codons 23 and 182 of the glnL coding sequence andpresumably results in a null mutation (Feng et al. supra).

The time course of the β-galactosidase (β-gal) activity was measured inwild-type and in the glnL mutant. The glnAp2-β-gal activity increases ina time-dependent fashion similar to the excreted acetate concentrationfrom the glnL host (JCL1596), whereas no induction of promoter activitywas found for the isogenic wild-type control (JCL 1595).

TABLE 1 β-galactosidase activity of glnAp2-lacZ β-galactosidase activity(nmol/min-mg protein) 6 hours 11 hours glnAp2-lacZ in WT (JCL1595) <100~100 glnAp2-lacZ in glnL (JCL1596) ~700 ~1500 P_(lac)-lacZ in (VJS632)~500 ~550

Thus, in the absence of glnL, glnAp2 is capable of responding to theexcess carbon flux that is indicated by acetate excretion. As the cellsapproached the late-exponential phase, the biosynthetic requirementdecreased and the cells began to exhibit an excess carbon flux, asdemonstrated by the increased generation of acetate. At this point, atapproximately 6 hours, unexpectedly glnAp2-β-gal activity began to riseto (˜700 nmol/min-mg protein, see Table 1) whereas glnAp2-β-gal activityin the wild-type strain (JCL 1595) was relatively low and remainedconstant throughout (˜100 nmol/min-mg protein, Table 1). After more than10 hours, glnAp2-β-gal activity in the absence of glnL was a remarkable˜1500 nmol/min-mg protein (Table 1). The induction profile of glnAp2 isalso in stark contrast to that of the lac promoter (P_(lac)).Chromosomal P_(lac) activity in strain VJS632 (lac⁺) rapidly increasedafter induction with IPTG (isopropyl-β-D-thio-galactopyranoside) andachieved a constant level of expression in the cell (−550 nmol/min-mgprotein, see Table 1), which is independent of the growth phase.

Usage of the glnAP2 promoter in E. coli in a Heterologous Fusion to ppsand aroG

Expression of two different metabolic enzymes, phosphoenolpyruvatesynthase (pps) and 3-deoxy-D-arabinoheptulosonate 7-phosphate (DAHP)synthase (aroG) were placed under the control of the glnAp2 promoter. Ascontrols, these same two proteins also were overexpressed from the tacpromoter (P_(tac)), which exhibits static control, under the samegenetic background and environmental conditions. Standard methods ofexpressing pps leads to growth retardation (Patnaik et al. (1992) JBacteriol 174:7527–7532).

Plasmid pAROG was constructed by cloning a PCR fragment containing aroGpRW5tkt into the EcoRI-BanHI sites of pJF118EH. Plasmid pPS706 has beenpreviously described in Patnaik et al. supra. Both plasmid express therespective genes under the P_(tac) promoter. The PCR fragment containingthe glnAp2 promoter was cloned into the EcoRV-EcoRI sites of plasmidspAROG, and pPS706 to generate plasmids p2AROG3, and pPSG706,respectively containing the respective genes under the glnAp2 promoter.

Host strain BW18302 (lacXglnL2001) was transformed with all fourplasmids. The strains with the respective plasmids were grown in M9salts-glucose media. Growth was compared after 5 hours.

TABLE 2 Growth of Overexpressing Strains OD₅₅₀ after 5 hours growth Noplasmid ~0.5 P_(tac)-aroG ~0.5 glnAp2-aroG ~0.5 P_(tac)-pps ~0.12glnAp2-pps ~0.4

As previously demonstrated, overexpression of pps using P_(tac)-ppscaused marked growth retardation. However, the use of glnAp2unexpectedly resulted in close to normal growth (Table 2). After 15hours, proteins were isolated from each strain and analyzed on a 10%SDS-PAGE gel. At least 500% more pps protein was expressed when the ppsgene was controlled by the glnAp2 promoter compared to the P_(tac)promoter. In another surprising finding, AroG protein, whoseconventional overexpression is not overtly detrimental, was also atleast 300% more abundant in extracts from cells utilizing glnAp2promoter for expression compared to the P_(tac) promoter.

Production of Lycopene in E. coli by idi Overexpression

We reconstructed a recombinant lycopene pathway in E. coli by expressingthe genes dxs (coding for 1-deoxy-D-xylulose 5-phosphate synthase) fromE. coli, gps (coding for geranylgeranyl diphosphate (GGPP) synthase)from Archaeoglobus fulgidus, and crtBI (coding for phytoene synthase anddesaturase, respectively) from Erwinia uredovora. These genes wereinserted into pCL1920, a low-copy-number plasmid, to form pCW9, andsimultaneously overexpressed.

We used the glnAp2 promoter to control the expression of idi(isopentenyl diphosphate isomerase). Constructs containing the idi genewere derived from a promoterless vector, pJF118, The glnAp2 promoter wasinserted to form p21DI. As a control, the P_(tac) promoter was insertedto form pTacIDI. These plasmids were separately introduced into a glnLstrain (BW18302) containing pCW9. The p21DI-containing strain(glnAp2-idi) produced 100 mg L⁻¹ lycopene after 26 h in a defined mediumcontaining glucose. The strain containing P_(tac)-idi on the other hand,produced only a small amount of lycopene, (<5 mg L⁻¹) under identicalconditions. Additionally, the p21DI strain produced almost threefoldless acetate than pTacIDI, which indicates that the carbon flux toacetate was being rechanneled to lycopene.

TABLE 3 Carbon yield of lycopene formation in batch cultures of E. coli.Lycopene Carbon yield on glucose (mol C/mol C) Host only (BW18302)0.0000 +pTacIDI (Ptac-idi) 0.0003 +pTacIDI (Ptac-idi)/pPS184 (Ptac-pps)0.0012 +p2IDI (glnAp₂-idi) 0.014 +p2IDI (glnAp₂-idi)/pPSG184(glnAp₂-pps) 0.022Use of pps to Enhance Lycopene Yieldpps was overexpressed from gnlAp2 from another compatible plasmid,pPSG18 while the remainder of the lycopene pathway (dxs, gps, crtBI) wasexpressed using pCL1920. Coexpression of pps and idi with the lycopenepathway increased the final titer of lycopene by 50% and caused theproductivity to increase by threefold, from 0.05 mg mL⁻¹h⁻¹ to 0.16 mgmL⁻¹ h⁻¹ (Table 3) This is in contrast to the companion straincontaining both pTacIDI and pPS 184 (P_(tac)-idi+P_(tac)-pps), where nosignificant improvement in yield was observed and substantial growthinhibition occurred.Additional Host Cells for Lycopene Production

The pykF::cat and pyk::kan alleles were introduced into a wild-typestrain, in order to generate two single mutants (JCL1610 (pykF) andJCL1612 (pyk4)) and one double mutant strain (JCL 1613 (pyk FpykA))(Ponce et al. (1995) J Bacteriol 177:5719–5722). The double mutantstrain was able to achieve a final lycopene titer of about 14 mglycopene/g dried cells, while the single mutant strains each obtainedlycopene titers of about 2.5 mg lycopene/g dried cells. The single pykmutants produced lycopene at a level similar to the wild type strain, ˜4mg lycopene/g dried cells. Further, overexpression of Pck,phosphoenolpyruvate carboxykinase, increased the final lycopene titer byabout 3-fold. Overexpression of Ppc, phosphoenolpyruvate carboxylase,reduced lycopene production by about 30%.

OTHER EMBODIMENTS

A number of embodiments of the invention have been described.Nevertheless, it will be understood that various modifications may bemade without departing from the spirit and the scope of the presentinvention. Accordingly, other embodiments are within the scope of thefollowing claims. For example, all homologs of the mentionedpolypeptides and genes are within the scope of this invention.

1. An E. coli host cell comprising a first expression cassettecomprising a promoter and a nucleic acid sequence encoding isopentenyldiphosphate isomerase, geranylgeranyl diphosphate synthase,1-deoxyxylulose 5-phosphate synthase, a phytoene synthase, or a phytoenedesaturase the nucleic acid sequence being operably linked to thepromoter which is bound by ntrC such that the promoter is regulated byacetyl phosphate in the absence of nitrogen starvation, wherein the cellis lacking a functional glnL histidine protein kinase gene.
 2. The hostcell of claim 1 wherein the host cell further comprises a nucleic acidsequence encoding a phosphoenolpyruvate synthase.
 3. The host cell ofclaim 1 wherein the enzyme is isopentenyl diphosphate isomerase.
 4. Thehost cell of claim 1 wherein the enzyme is geranylgeranyl diphosphatesynthase.
 5. The host cell of claim 1 wherein the enzyme is1-deoxyxylulose 5-phosphate synthase.
 6. The host cell of claim 1wherein the promoter is glnAp2.
 7. A kit comprising (i) a nucleic acidsequence containing a promoter bound by ntrC such that the promoter isregulated by acetyl phosphate in a defined bacterial host cell, and acoding sequence that encodes; isopentenyl diphosphate isomerase,geranylgeranyl diphosphate synthase, 1-deoxyxylulose 5-phosphatesynthase, a phytoene synthase, a phytoene desaturase, or a lycopenecyclase and (ii) the defined host cell which is an E. coli host cellgenetically modified by deletion or inactivating mutation of the glnLgene.
 8. The kit of claim 7 wherein the promoter is the glnAp2 promoter.9. A method of producing a lycopene in a bacterial host cell, the methodcomprising: providing the host cell of claim 1; and expressing a1-deoxy-D-xylulose 5-phosphate synthase, a geranylgeranyl diphosphatesynthase, a phytoene synthase, and a phytoene desaturase in said hostcell, at least one of which is expressed from the first expressioncassette.
 10. The method of claim 9 further comprising culturing thehost cell under nitrogen rich conditions.
 11. The method of claim 10 inwhich the culturing comprises growth to late logarithmic growth.
 12. Themethod of claim 9 in which at least 5 mg L⁻¹ of lycopene are produced.13. The method of claim 10 in which the promoter is glnAp2.
 14. Themethod of claim 11 in which the promoter is glnAp2.